Arguments

An object of class pcm. For getIC,
if parameter p is followed, x should be an object of matrix.
For pcm2pfm, x also could be an object of matrix.

y

Not use.

p

p is the background frequency.

n

how many spaces should be added.

b

logical value to indicate where the space should be added.

background

a "numeric" vector. The background frequency.

t

numeric value of information content threshold for trimming.

...

Further potential arguments passed to plotMotifLogo.

Methods

addBlank

signature(x="pcm", n="numeric", b="logical") add space
into the position count matrix for alignment. b is a bool value, if TRUE, add
space to the 3' end, else add space to the 5' end. n indicates how many
spaces should be added.